AutoAF mode extends the CFP (closest focus priority) of the Group Area modes across the entire AF search area. As in the Pro DSLRs (D6, D5 Triumvirate), AutoAF is very useful in the Z9 to track an erratic subject against distant backgrounds, open water etc
AutoAF: clutter in the scene, including twigs etc, will often discombobulate AutoAF off the subject, although the Z9 subject detection buffers this tendency somewhat. But subject detection has its limits, obviously. However, when it works, Auto is stickier on subjects closer to frame borders, compared to 3D;
3D Tracking: works better in the Z9 at tracking the subject within/against clutter, especially with Subject Detection. IME the D6 AF modes follow this general rule, although D6 subject detection is weaker, its AF modes are far less likely to grab the background (thanks to the full set of cross-type sensors).
So as a rough rule, the background/habitat structure determines whether to Hand off from a tighter AF mode (I use a Custom Area) to AutoAF or 3D.
Any AF mode will struggle if the subject is too small in the frame.